Foodborne infections are estimated to cause >76 million illnesses, 300,000 hospitalizations and 5,000 deaths in the U.S. each year. Salmonella, Campylobacter, Shigella, and enterohemmorhagic Escherichia coli (EHEC) cause most infections, particularly in children <5 years of age. These four pathogens contribute to a wide range of illnesses including both bloody and non-bloody diarrhea, but also cause kidney failure, neurological disorders and death in some cases. For most enteric bacterial pathogens, the disease process is initiated by transmission to a susceptible host, passage through the gut, and attachment to host epithelial cells lining the gastrointestinal tract Most pathogens have evolved a variety of specialized mechanisms that enhance this process, and in several cases, specific genotypes have been shown to cause more severe disease than others. While bacterial characteristics are clearly important, the role of the host in disease pathogenesis should not be overlooked, as the interplay between different pathogens and host microbial communities is likely to be important for disease development. Here, we propose to use pyrosequencing combined with metagenomics to investigate the impact that these four common diarrheal pathogens have on the composition and function of the intestinal microbiome. We will analyze stool DNAs from 200 healthy individuals without diarrhea and make comparisons to 800 individuals with diarrhea caused by EHEC, Salmonella, Campylobacter, and Shigella. The specific aims are: (1) Demonstrate that the composition, diversity and structure of the intestinal microbial community and the presence and expression of key virulence and antibiotic resistance genes impacts diarrheal disease caused by different enteric bacterial pathogens; (2) Determine that enteric disease profoundly affects the abundance of community members, the production and expression of microbiota by-products, and the distribution and diversity of functional marker genes (e.g., short chain fatty acids); and (3) Demonstrate that specific genetic and phenotypic characteristics of different enteric pathogens will more frequently and drastically alter the microbiome in patients with enteric disease. The proposed study will enhance our understanding of how the microbiome is impacted by infection with common enteric pathogens while controlling for gender, age, microbiota compositional and functional profiles, host immune responses, and bacterial characterisfics. Beneficial microbial communities, microbes and microbial products important for preventing enteric disease will be identified, which in turn, could guide future prevention and treatment strategies.